Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA

Many studies have revealed pathways of epigenetic gene silencing by Polycomb Repressive Complex 2 (PRC2) in vivo, but understanding molecular mechanisms requires biochemistry. Here we analyze reconstituted human PRC2-nucleosome complexes. Histone modifications, the H3K27M cancer mutation, and inclusion of JARID2 or EZH1 in the PRC2 complex have unexpectedly minor effects on PRC2-nucleosome binding. Instead, protein-free linker DNA dominates the PRC2-nucleosome interaction. Specificity for CG-rich sequences is consistent with PRC2 occupying CG-rich DNA in vivo. Intriguingly, PRC2 preferentially binds methylated DNA via AEBP2, suggesting how DNA- and histone-methylation collaborate to repress chromatin. RNA is known to inhibit PRC2 activity. We find that RNA is not a methyltransferase inhibitor per se, but instead sequesters PRC2 from nucleosome substrates; this occurs because PRC2 binding requires linker DNA, and RNA and DNA binding are mutually exclusive. Together, we provide a model for PRC2 recruitment and a straightforward explanation of how actively transcribed portions of the genome bind PRC2 but escape silencing.